pypreprocess is a collection of python scripts for preprocessing (motion correction, spatial normalization, smoothing, etc.) fMRI data using nipype's SPM and FSL interfaces. It also contains utilities for automatic QA like registration checks (using nipy.labs), and template-based html report generation using (tempita, jquery, and home-grown css).

Check out the [wiki](https://github.com/neurospin/pypreprocess/wiki).

First of all, you will need to have the following (standard) tools installed on your system: * git * pip

The requirements/dependencies (nipy, nipype, traits, nibabel, nisl, etc.) are documented in the *dependencies.txt files.

To install these dependencies in one go, simply chdir to the directory containing this README and then type (in your terminal):

python install_depenencies.py

We have written some examplary scripts for preprocessing some popular datasets.

cd to the pypreprocess/examples directory, and run the following command:

python nipy_glm_spm_auditory.py spm_auditory spm_auditory_runs/

Now open the file spm_auditory_runs/subXYZ/report.html in your browser (firefox), to see the generate report (QA).

Improve on this README.